Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards, Claire Pujoll Paris, France library(marray) library(limma) ....... Rawdata <- read.GenePix(targets=Macro_Mono_targets,skip=107) design<- cbind(individual=c(0,0,1,1,2,2,3,3,4,4,5,5), dim1=c(1,0,1,0,1,0,1,0,1,0,1,0),dim2=c(0,1,0,1,0,1,0,1,0,1,0,1)) fit <- lmFit(normdata@maM, design) contrast.matrix<-makeContrasts(dim1vsdim2=dim2-dim1, levels=design) fit2 <- contrasts.fit(fit,contrast.matrix) fiteb <- eBayes(fit2) Toptable <- topTable(fiteb,number = 10600,genelist=maGeneTable(normdata), sort.by="P", resort.by= "M", adjust="BY") write.table(Toptable,file="RNG_Best_10000genes.txt", row.names=FALSE, col.names=TRUE, sep="\t") best regards [[alternative HTML version deleted]]
Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards, Claire Pujoll Paris, France library(marray) library(limma) ....... Rawdata <- read.GenePix(targets=Macro_Mono_targets,skip=107) design<- cbind(individual=c(0,0,1,1,2,2,3,3,4,4,5,5), dim1=c(1,0,1,0,1,0,1,0,1,0,1,0),dim2=c(0,1,0,1,0,1,0,1,0,1,0,1)) fit <- lmFit( normdata@maM, design) contrast.matrix<-makeContrasts(dim1vsdim2=dim2-dim1, levels=design) fit2 <- contrasts.fit(fit,contrast.matrix) fiteb <- eBayes(fit2) Toptable <- topTable(fiteb,number = 10600,genelist=maGeneTable(normdata), sort.by="P", resort.by= "M", adjust="BY") write.table(Toptable,file="RNG_Best_10000genes.txt", row.names=FALSE, col.names=TRUE, sep="\t") best regards [[alternative HTML version deleted]]
I have a question about R. I would like to simulate a following model. Xt+1=Xt(1+b) "b" is a random variable. to get 10 plots. I haven't used R program, how can I code on R to run above simulation? It rould be grateful if you kindly answer... thank you. yumiko watanabe